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Using Python and Fabric for analyzing brain signals on OSG connect
Scott ColeNeurosciences Graduate Program
UC San Diego
Outline● Brain rhythms
● Running python on OSG
Large-scale brain recordings
● Healthy humans● Patients● Animals
● Sampling: 500-30000 Hz● Duration: 1 hour - 1 week● Channels: 1 - 250+● Several GB per subject
Neural oscillations (a.k.a. Brain rhythms)
Fourier Transform-based analysis
Fourier Transform-based analysis
Custom analysis in Python
1. Clone tutorial (.py, .sh, & .submit) from GitHub
2. Create python virtual environment
3. Transfer input data to Stash
4. Compress personal libraries
5. Submit job
6. Transfer output and plot results
Steps 1-6 with Fabric
NOTE:Not Python 3 compatible
1. Prepare files (clone repo)2. Create virtual environment3. Transfer input data4. Prepare (compress) local libraries5. Submit job6. Transfer output data
Summary
San Diego Union-Tribune
Thank you